Season ?: The Captain and the Yard
by Escadia
Summary: Season ?: Episode 2: The Doctor and Jenny arrive on Earth to find themselves promptly arrested. Now they have to team up with a friend to prove the Doctor's innocence against an old enemy with a new face.
1. Arrivial

**Author's Note: Sorry about how short this is. I reached the point I planned to end the chapter and found I had only written just over 3 pages instead of my usual 4 to 4 1/2... I'll make it up somehow.**

The doors banged open. Dad and Jenny dashed in and forced them shut. Breathless, they grinned at each other for a moment, before dissolving into laughter. Almost immediately someone started banging on the outside. The TARDIS seemed to hum inquiringly as Dad, trying to regain his composure, worked his way up to the controls.

"Okay, so, what have we learned today?"

"Well," Jenny said, deciding the floor would make a great seat as she recovered, "pretty much, if you're ever asked by omnivorous cannibals with four arms to join them in a 'hunt', say no."

The banging grew louder as the being outside was joined by several of its fellows.

"No, no," Dad said, shaking his head. "That's rather rude. First you have to ask which side you're supposed to be on, the hunter or the hunted. If it's the former, you can refuse on moral grounds."

"And if it's the later?"

"You get a head start."

"So it doesn't matter?"

"No, but manners are important."

"Since when do you use manners?"

He paused from fiddling with whatever he had been fiddling with. "There's an old saying, used by a lot of parents. Do as I say, not as I do."

"Yeah, sure, because that's not hypocritical at all," she said slowly climbing to her feet. She motioned back to the door. "Can they get through that?"

Dad shook his head. "That door has held back things far worse than hungry savages."

"Good." Jenny mounted the first step up to the controls, holding on the railings with either hand. "So, not pissing off the locals before the big feast, should I file that under 'Common Sense' or 'Don't Feed a Dragon Ham'?"

"Okay, first of all, that was not a dragon," Dad said, wandering around the other side of the control column. "Second of all, why didn't it like the ham? I mean, what, are giant, flying, fire breathing lizards – okay, it was a dragon – are they too good for a roast of ham?"

Jenny shook her head. "It probably didn't help that you ran all the way back to the TARDIS carrying it."

"What?" he protested, shrugging. "That was a good ham. If he didn't want it, I'd eat it." He leaned against the railing. "I mean, I gave him the chance. I didn't even go back to grab it till his third pass."

"You know, I'm really glad no one else was there to see that."

He grinned. "What's the point in being a dad if you don't get to embarrass the kids from time to time?" He glanced at the door where the pounding was persisting. "That's getting a little annoying," he said, pushing himself off the railing and reaching out to the controls.

The TARDIS groaned and wheezed, shaking for a moment as the banging faded away.

"Better," Dad said, smiling at her again and leaning back up again the railing. "So, where to next? There's a planet called Barcelona. They've got dogs with no noses. Sad little things, they never get to smell. Or chase cats. They don't have cats there for some reason; I think it's against the law. Something about the dogs being allergic to their dander, which doesn't make much sense, because they still don't have noses."

Jenny contemplated it for a moment, staring down at the steps. Finally, she looked up. "What planet is Donna from?"

If she hadn't been looking right at him, she might have noticed the near imperceptible shift in his defenses that came with bad memories. "Earth," he said after a moment of hesitation. He quickly busied himself with something on the control panels, another defensive sign.

"What's it like?"

"Oh, it's wonderful," he said sincerely. "A little tiny blue planet with nothing special about it, yet everything in the universe seems to pale next to it. I blame the humans. Clever apes. Well, okay, stupid, primitive, obsessive, and proud apes, but oh so clever. Recently I was in a country called America and tried some 'Cheese Fries'." He gave her an almost giddy look. "They were literally chips covered in cheese. I'd heard of them, but that was the first time I'd ever tried them. They were amazing. Granted, they probably had enough grease in them to take a decade off my life, but the flavor. Actually, I don't think there's anything you couldn't improve by covering it in cheese." He paused. "Except broccoli. Never was a big fan of broccoli myself, not even during that vegetarian phase a few years back. Or cauliflower. They're just like little trees, it's weird."

Jenny grinned. "Can we go there?"

Dad hesitated again. He removed his hands from the console and turned to her. "Jenny, you can't ever see Donna. Never."

Letting go of the handrails, Jenny climbed the last few steps up to the control deck. "Why not?"

Dad sighed. "It's complicated." He turned back to the consoles, fiddling again for a moment before continuing. "Donna absorbed my mind. Well, okay, not my actual mind, but a copy. Still, she knew everything I knew. And that was the problem. She had a Time Lord mind in a human brain. It was too much, far too much, for her to handle. She started to short circuit, burning her mind out." He looked at her. "I couldn't erase her memories, so I suppressed them. She doesn't remember anything, not me, not you. And if she ever does, she will die."

The silence hung in the air.

"So do you understand?" Dad finally asked. "Do you understand why you can never see her again?"

Jenny nodded slowly.

"Do you still want to go to Earth?"

"Yes."

Dad crossed his arms. "Why?"

"It was her homeworld." Jenny smiled weakly. "Donna is the only other person I ever really met. She accepted me. She was important. Even if I can't see her, I want to see where she came from."

Dad gave her a kind smile in return. "One trip to Earth, coming up." He turned back to the controls. "Pretty simple. Press this here, twist that, don't forget to flip these, very important those. I don't exactly remember what they do, but they're important."

The TARDIS groaned. Jenny was smiling widely.

"Pull this, shift this here, press this, this, this, and this, in that order, twice, then do it backwards, and finally, hit that." He nodded at her. "Go on, my hands are full over here."

Jenny pressed the large yellow button. The TARDIS shook, jerked, then settled in.

Dad pushed past to the exit. "Well, here we are." He grinned again, leaning against the doors. "Planet Earth." He turned around, threw the doors opened and stepped out. Jenny jogged out after him.

And came to a sudden halt as an assault rifle was pressed in her face.

Dad's hands were already up. Slowly, she raised hers.

"This happen to you a lot?" she asked.

"No. Well, okay, occasionally, well, less than occasionally, but certainly every once in a while. I'd say in a blue moon, but I think it happens a bit more often than that."

"Quiet," a man holding a rifle said. He was dressed in black body armor and was wearing a red beret. In fact, all six of the men sounding them were dressed like that. Definitely soldiers of some sort.

A woman, perhaps in her late thirties, stepped to the front. Unlike the others, she wasn't wearing any armor. Instead, she was dressed in a sharp dress uniform. She paused, looked both of them up and down. "Doctor," she finally said curtly, settling her gaze on Dad.

"Colonel," he answered, glancing around. "You know, while I certainly appreciate you lot changing up your greetings, give life a little variety, and while I still really didn't like the other one, I think I do prefer when UNIT threw up solutes instead of guns."

"I'm placing you under arrest, Doctor."

"Oh, okay. Out of curiosity, for what?"


	2. Interrigation

It was a small room. The walls were white, the floor had grey tiles, there was a windowless wooden door, and built into one of the walls was a large mirror that she had her suspicions about. They were both sitting on one side of a plain metal table. A third chair sat empty opposite them. Dad was leaning forward in his chair, his chin in his left hand, the fingers of his right tapping impatiently. Lying on the table next to him was a plate of some sort of food Jenny had never seen before.

She picked one of them up. "What are these?"

"Pastries. Doughnuts, to be exact."

She bit into the doughnut. "This is really good, I like it."

"Makes sense, of course you do."

She gave him a hurt look. "What's that supposed to mean?"

He glanced at her, lifting his chin off his hand slightly. "It's chocolate. You're a girl. Girls like chocolate." He frowned. "What did you think I meant? Because there really wasn't supposed to be a lot of subtext in that."

She slowly put the doughnut down.

The door opened suddenly. A uniformed man with a red beret entered with a set of folders tucked under his arm. He was older, with graying hair and wrinkles at his temples, but he was still very muscular and moved with purpose.

"Oh, a general," Dad said, shifting his gaze. "I feel like I should be honored."

"Don't be," the man said in a hoarse, accented voice. "I'm General Kennan Sloane. I'm in charge of your investigation."

"I surmised as much." Dad leaned back. "I would rather like to know what exactly this investigation is about. The colonel wouldn't tell me. And you know, it's generally considered rather rude to arrest someone and not at least tell them a reason why. Even if it's a fake reason."

Sloane settled down in the seat across from them. "You seem rather at ease here, Doctor."

"I didn't do anything wrong." He paused. "Lately. At least, not that I know of." He grinned. "And you, General, are avoiding my question."

"Well, it's generally considered rather rude for the suspects to ask the questions."

"Okay, well, I give you that. However, seeing as you lot aren't doing this thing right, I feel I have certainly liberties." He pointed upward. "Not only are you not telling me why you've arrested, you're using fluorescent lighting. Bright fluorescent lighting. The best interrogation I've ever seen had a single dim bulb hanging from the ceiling, making it near impossible to see into the corners. Now that, that was intimidating." He paused. "Then again, that was in the Nineteen Twenties. Or maybe a movie. I can't quite remember."

"I'm not laughing, Doctor," Sloane said quietly.

"I'm actually being kind of serious."

Sloane adjusted the folders on the table in front of him. "Doctor and-" he let it trail off, looking at her.

"Jenny," she said with a meek look.

"My daughter," Dad supplied.

"Daughter." Sloane scowled slightly. "I see. It seems we need to update our files." He glanced at the mirror. "Doctor, you and your companions have been of great service." He returned his gaze to Dad. "Both to this organization and to the world in general. That is the reason you are in this room and not a cell awaiting your execution."

"Execution?" Dad leaned forward again. "Britain doesn't do executions."

"We are not a British organization. The Unified Intelligence Taskforce is international, and deemed with the responsibility and power to take care of any extraterrestrial threat, including the use of executions."

"Oh, yes, because you lot are always there to take on whatever the biggest and baddest threats to humanity."

Sloane glared at him. "We are limited by funding, Doctor, and we don't have a time machine to go back and fix our mistakes."

"Well, it doesn't quite work that way. Fixing your lot's mistakes are fine, fixing my own would probably tear a hole in all of space and time."

"We are not as helpless as you make us out to be."

Dad snorted. "You're not? To be honest, sometime I'm surprised you manage to get your shoes on right. Even your best, like the Brigadier, insisted on shooting everything, even those he knew they were immune to bullets."

"I assume you're speaking of Sir Alistair Lethbridge-Stewart and would kindly warn you not to insult the hero of our organization."

"Insult him? The Brigadier was a great man, but there were definitely situations he made harder by insisting on being a soldier."

Sloane opened his mouth to speak again, but the door flew open. The man was tall, with a square jaw and a cleft chin. "Okay, this has to be the right room, because the last two were empty."

"Who are you?" Sloane snarled. "And how did you get in here?"

"Captain Jack Harkness," he said, holding out a hand. "I let myself in, hope you don't mind."

A vein was sticking out of Sloane's temple. Harkness let his hand drop, and looked over at Dad and Jenny. He studied them for a moment. "Doctor," he said, finally pointing at Dad. "You've regenerated again."

"It happens," Dad said with a shrug.

Sloane found his voice again. "This is not a Torchwood matter!" Two soldiers appeared in the doorway, holding their guns ready. "You will leave here immediately!"

"I'm not here on the behalf of Torchwood," Harkness said with a charming smile. "I thought I'd drop by and provide a character witness."

"This is not a trial," Sloane snapped.

"No, you're just planning on killing me," Dad said, cocking his eyebrows inquisitively. "Did I miss the trial? It's not nice to hold them when the accused isn't present. Or to not tell the accused what his being charged with."

"They haven't told you?" Harkness asked curiously.

"That's enough!" Sloane boomed. "I will not let either of you turn this investigation into a mockery. Harkness, leave or I will have you thrown in a jail so deep not even your pathetic teleporter watch will get you out."

"It's a Vortex Manipulator," Harkness said, sounding a little offended.

"Out!"

"I'd like him to stay," Dad interrupted. "It's a rather hostile environment here and it'd would be nice to have a friendly face for support."

"What about me?" Jenny asked.

"Well, okay, a friendly face that knows what's going on."

Sloane looked livid, but finally shook his head with resignation. "Fine. Get the captain a chair," he barked at his soldiers. Both of them hurried off.

"So, Jack, can you tell me what this is all about?" Dad asked.

"I don't know the specifics," Harkness admitted. "UNIT's been keeping it rather close to their chest. But there have been several incidents that are rumored to have been committed by you."

"You're here, Doctor," Sloane interrupted as a soldier brought another chair in, "for two counts of sabotage, four counts of kidnapping, ten counts of extortion, twenty-two counts of theft, and most importantly, one hundred and forty-eight counts of murder."

Dad was quiet for a moment. "That's a lot. Although, I don't think I've ever extorted someone before. I mean, I suppose I've black mailed a couple of people in my time, but does that count as extortion?"

Sloane crossed his arms. "Usually, people's first reaction is to deny things."

"Well, I'm not admitting to anything," Dad said with a shrug, "but I have had a rather sordid past."

"Including murder?"

Dad's eyes narrowed. "I'm not necessarily proud of it."

"Three of the murder victims were children."

Dad shifted slightly, his eyes going very dark. "What happened?" he asked, his voice again taking the much older and colder tone that he used when he was serious.

Sloane shifted through the folders and handed one to Dad. "About two months ago, a laboratory that specialized in developing new, durable high speed circuitry was commissioned to develop a new board by an unknown party. They finished about three weeks back. The night they finished, there was a fire, killing twenty-seven men and women. The lab has a large quantity of chemicals it used to score the circuits. It's rather combustible. When the fire reached it, it destroyed a rather large section of the lab." He paused. "The children were in a car outside. They were there to pick their father up like they did every night. It was their mother that called it in. She had left them in the car while she used her cell to contact the fire brigade." He paused a second time. "The explosion sent an I-beam into their car. Due to the speed and angle it was traveling, it twisted the car around itself and flipped it over, killing everyone inside."

Dad was flipping through the file almost impossibly fast. "How does this connect to me?"

"Several of UNIT's contacts link this to a new group that's been stirring up trouble in Britain's underground. They're rather violent and reckless, and led by a man who claims to be the 'Doctor'."

"I am many things, General, but I've never been, nor will ever be, a crime lord."

"To be honest, Doctor, I'd be inclined to agree. You've done far too much for this world to be bothered with something as petty as a crime spree. I know that many of UNIT's soldiers would not only lay their lives on the line for you, but help you get whatever you might need for a project, no matter how rare or expensive."

Dad tossed the folder aside. "What changed your mind?"

"There's a pattern." Sloane tapped the folders he still had. "Not a single one of these is older than six months and they're all linked crimes. They've all had to do with either the procurement of money or technology. And they've all had a certain flare to them, an almost careless and arrogant sense of superiority about them. Usually criminal like that get caught quickly. They make mistakes. They're only human. This 'Doctor', on the other hand. All those crimes and all those deaths, used up so carelessly, but there were almost no mistakes."

"Almost."

"Yes," Sloane said with a nod, "almost. We caught a break." He pulled out another folder. "Gabriel Ojeda. A Spanish immigrant and perpetual thorn in my side. He dealt in illegal technology, human and otherwise."

"I know him," Harnkess said. "We needed to repair Torchwood Three at one point and he helped supply us."

Sloane scowled. "That's part of the reason he was so hard to control. He had so many customers that claimed to benefit from his connections that our leads got thrown off every time we tried. We'd get close and someone would help him out."

Jenny wouldn't say that Harnkess's shrug was meek, she honestly didn't know if he could pull off meek, but it was close.

"Eight days ago, Ojeda was found dying in his flat after several shots were heard," Sloane continued. "He died on the way to the hospital. Since I had spent several years trying to track him down and his deals with high level alien tech made him a prime target for this crime spree, we made sure to cover his flat inch by inch. Near the back entrance, we found a small amount of blood, no more than a drop. The techs assure me there must have been more, but it was cleaned up. However, with the noise of several neighbors in the halls and the sirens of the police arriving, whoever had cleaned up must have missed it."

"So Gabriel's killer took a bullet," Harkness said.

Sloane nodded. "We have some of the fastest computers and most advanced testing machinery in the world in this building. We confirmed the blood wasn't human. We made sure to double check.

"Doctor, the blood was yours."


	3. DNA

**_Special Note: Finally! In case you're wondering why it took so long for the chapter to be published, it's because there was an error preventing me from publishing anything. I've spent the week and a half trying to get it to work. Between that and normal life, I didn't have a chance to get this last Tuesday's chapter ready. This, in case you were wondering, this chapter was supposed to go up 3/15._**

**Author's Note: Wow, it wasn't till I was reading this I realized how heavy it is on the Doctor's dialogue. Maybe I'm just being paranoid...**

Jack glanced back at the Doctor, who was still frowning. It always took him a little while to get used to his new faces. This one was pointier than the others he had seen. But no matter how much they changed, there was something always inhuman about them when he was angry.

And he was angry.

His pretty blonde companion-Jack hadn't heard her name yet-looked worried. That was good. That meant she had been traveling with him long enough to know the warning signs. The Doctor was amazing, downright spectacular, but he was also terrifying.

"How certain are you that it's mine?" the Doctor asked quietly.

"Very certain," General Sloane said with a slight nod. "The techs assure me that it's a match."

"A match to what? Last I checked, UNIT wouldn't have anything to compare it too."

"Actually, we do."

"Really? How?"

General Sloane looked distinctly uncomfortable. "Back, early in your partnership with UNIT. You weren't conscious and our scientists were curious about the difference between our two species."

The Doctor put Ojeda's folder down slowly. "Excuse me? When was this?"

"Does it really matter?" General Sloane snapped.

The Doctor leaned back, scowling. "What's the motive?" he asked after a moment.

General Sloane hesitated.

"You don't have one yet?" Jack asked.

"No."

"Then how can you condemn him to death?" the pretty blonde asked.

General Sloane shifted slightly. "Motive is one of the things we wish to find out." He fixed his gaze on the Doctor. "There is no question that you were, or at least will be, in that room."

"I question it," the Doctor murmured. "It doesn't make any sense, General," he said louder. "I have no use for money. I'm crossing back and forth in time so much that it doesn't matter. I couldn't very well buy any chips with a couple Roman denari, nor could I use the British Pound in the year Pear/8/Pi/Pegasus."

"I don't think I've ever been to that century," Jack mused.

"And what point would I have with technology," the Doctor continued. "I already posses the most advanced ship in all of space and time. Which, actually, I did kinda steal. Well, I borrowed it with every intention of returning it someday."

"And what if you lost your ship?" General Sloane asked.

The Doctor snorted. "Lose the TARDIS? I doubt that's even possible. Even if I will, I haven't yet, meaning you're trying to prosecute me for a crime I haven't even committed yet."

General Sloane let out a sigh. "Then what am I supposed to do, Doctor?"

"You're going to let me do what I do best," the Doctor answered. "I need to see all the evidence you've collected and talk to the techs that processed it. I'm also going to need a full list of schematics of what's been stolen so I can try and figure out what this fake 'Doctor' has been working on."

"You honestly expect me to let the prime suspect work on his own case?" General Sloane blustered.

The Doctor leaned forward, jabbing one finger at the general. "Yes, you are. Because, to be perfectly honest, in my very long life, I have committed every crime you've accused me of and more. But they were to protect people. I cannot abide someone who squanders the lives of innocents, of children, and I will stop them. So you can either help me or completely stay out of it, but I promise you, if you try and stand in my way, I will tear you down."

General Sloane's eyes had narrowed. "I don't respond well to threats, Doctor."

"Then consider it a warning."

General Sloane shook his head. "No, I believe I'm going to have to call your bluff here, Doctor. Even if you weren't currently my prisoner, separated from your ship, your screwdriver, your psychic paper, and anything else that could even remotely be used in an escape attempt, you are still just a single man. UNIT is far too powerful to be torn apart by you."

The Doctor's grin was more than a little sinister. "Harriet Jones thought the same thing."

General Sloane opened his mouth as if to say something, but found himself at a loss for words.

"And I tore down her regime with six little words," the Doctor continued. "But she wasn't standing between me and the monsters. You are. So what do you think I'll do to you?"

General Sloane didn't answer. Instead, he glared at the Doctor's still outstretched finger, the vein at his temple bulging again. But however close he was to losing his temper, he managed to cling to it. "All right, Doctor," he said finally. "But you're going to do so under the supervision of both the techs and a full armed guard. You will not be permitted access to any of your belonging or your ship. Is that clear?"

"Of course," the Doctor said, letting his arm drop.

Their guard consisted of four men, well, three men and a very butch woman, almost smothered in body armor and each carrying enough guns, ammunition, and explosives to arm a small army. How they managed to carry it all, Jack couldn't quite figure out, but he wasn't surprised that every time they came to a stop, their guards used the walls for support.

The laboratory wasn't small, but it felt cramped, both due to the three of them and the general, plus the four guards, joining the two techs already working there, and that most of the room was taken up by several machines.

The lead tech, a Stanley Pritchard, introduced himself rather nervously to the Doctor. "I hope there aren't any sort of, well, kind of hard feelings, Doctor," he rambled. "I mean, I've always wanted to meet you, I just wish, that, well, you know, it hadn't been after I had, pretty much, kind of, found evidence that you, had, well, killed someone."

"Don't worry, I'm not convinced you have," the Doctor said, holding up a mollifying hand. "The general tells me that you are absolutely sure that the blood found matches mine."

"Well, mostly," Pritchard said, rubbing the back of his neck. "They aren't perfect, mind you, but, well, when you factor in both possible human error and contamination, plus the inherent difference that the blood is going to have when you figure that the control sample is from an earlier, well, I guess, version, or body, or c-"

"Regeneration," the Doctor supplied. "How does the test work?"

"Well, these aren't your general, run of the mill DNA tests, certainly a cut above the tests you'd find in some sort of paternity clinic. Several cuts above, dozens even." General Sloane gave him an impatient look, sending the young tech tumbling into his next sentence. "Well, you see, the normal test, it, well, compares the thirteen points that tend to differ between DNA, since the majority of it is, well, the same. These machines, however," he motioned around them, "are, well, much more advanced. It took years to map out a full strand of DNA, but these can do it in hours. They're about the most powerful machines you can find. I think they've been mostly reverse engineered from alien technology. It's too bad they can't play video games, because you'd never have any lag problems." As if suddenly realizing what he was saying, Pritchard blushed with embarrassment. "They, well, what they do is completely analyze and compare all the individual genes and can, well, give us an exact percentage difference between DNA. They're completely automated too, and can run up to four tests at a time. They make my job kind of easy. Not that my job's not important," he added hastily.

"What was the difference?" the Doctor asked.

"What?"

"What was the difference between my DNA and the DNA you found at the crime scene?"

"Point oh-oh-oh-oh-five percent."

The Doctor frowned. "That doesn't make any sense."

"Well, yeah, it does. It's well within the margin for error."

"Except there shouldn't be a margin of error." The Doctor glanced around the room. "Okay, look, the machine is automated, so how does human error factor in? You pop it in and it pops out the results. There's nothing for you to mess up. The only possible chances are to contaminate the sample with some of your lots' DNA or somehow damage the sample before it goes in. But then you'd be looking at a difference of ten, fifteen percent at least, which is far too large to cause our discrepancy.

"But at the same time, the discrepancy itself is too big. There is very little change to a Time Lord's DNA when he regenerates. The only things that change are the phenotypic genes, and those are such a small percentage of the strand."

"Phenotypic?" the pretty blond asked. "That's a new word."

"It means how you look," Jack said helpfully.

"I mean, look at you lot," the Doctor continued on as if they hadn't spoken. "How many genes do you share with a banana? Yet you look nothing alike. How many genes do you share with each other? The genetic difference between any two regenerations of a Time Lords shouldn't be any greater than point oh-oh-oh-oh-oh-oh-oh-oh-oh-oh-oh-oh-oh-oh-oh-oh-oh-oh-oh-oh-four-seven-three-oh-eight-five-five-seven-nine-three-five-four-five-oh-seven-eight. Approximately."

"That's approximately?" Jack asked with a low whistle. "I wonder how long the actual number is."

"I'd have to say seven another fifty-three times before I got to a new digit." The Doctor was staring at the machines thoughtfully. "Is it possible to look at the raw data of the strand?"

"You mean like the actual genes?" Pritchard asked. "Yeah, but, well, it'd take forever."

"I don't want to look at the entire thing, just the genes that differ."

"That's still a lot of information," the tech said doubtfully.

"I'm quick," the Doctor said dryly.

Jack chuckled. "Certainly explains things."

"Not that quick."

The Doctor settled down at a computer and started flicking through the screens. He sent Pritchard for a sheet of paper and started jotting down notes.

"I can see you don't really need me here anymore," General Sloane said gruffly. "Keep me informed." With that, he left.

Jack let his eyes wander back to the pretty blond. She was tall, not quite as tall as Donna had been, but taller than Rose or Martha. She had a certain military stance about her, probably enhanced by her green shirt and strict ponytail, and looked distinctly uncomfortable just standing around in an unfamiliar place.

"In all the rush, we never got introduced," he said, putting on his most charming grin and extending his hand. "Hi, I'm Jack."

She smiled back. It was a very pretty smile, and very innocent, clashing with her military bearing. "I'm Jenny."

"No Jack," the Doctor said, not even looking up from the screen. "Absolutely not."

"You know Doctor, sometime 'hi' really does just mean hi," Jack protested.

"Not with you it doesn't."

"Yes it can. I can say hi without there being ulterior motives."

"Kyoto."

Jack coughed. "That was different. And I really wasn't expecting the Imperial Guard to be there."

"Where's Kyoto?" Jenny asked curiously.

"It's in Japan," Jack said.

"Where's that?"

He studied her for a moment. "You're not from Earth, are you?"

She shook her head. "I'm from a planet called Messaline. Kinda. It's where I guess you can say I was born, but I didn't spend much time there."

"Never heard of it. Nice planet?"

She shook her head. "It was in the middle of a war. Or the tail end of one, I supposed."

"Let me guess. He showed up." Jack nodded toward the Doctor.

She smiled and nodded.

"He has a tendency to do that. Changes everything, of course."

"I've noticed," she said, mimicking the same dry humor the Doctor had picked up in this regeneration. Jack wondered if she had gotten if from him or he had gotten it from her.

"So, what's Torchwood?"

Jack spent the next hour telling her stories of his adventures, both with Torchwood and the Doctor. Part of him was hurt when she hadn't realized that he had traveled with the Doctor. But the Doctor never seemed to look back, so it wasn't surprising. She hadn't heard of Rose either, but apparently had met Martha and Donna somehow.

The Doctor finally leaned back. "How long does it take the machine to analyze a sample?" he asked.

"Well, it's about eight hours to complete a test," Pritchard said.

"How long till I can see it in a form like this?"

"You mean as raw data? About four."

Neither Jack nor Jenny realized what the Doctor was planning as he walked over holding a syringe. "Ow!" Jenny exclaimed as he stuck the needle in her arm.

"Hold still."

"You could have warned me."

"I didn't want to interrupt your conversation," he said, pulling the needle out.

"We weren't talking right then," she said in an annoyed voice.

"Right, sorry." He handed the sample over to Pritchard. "Since we have time to kill, I think I'm going to look over those schematics."


	4. Genes

**Author's Note: MOTHER $%#& ON A $#% WITH *%&# #%& #&*$#&^ AND RACCOONS %#$*& IN *$#&^# FOR *$%#& WITH %$^#*% SIDEWAYS! Honestly, if it's not one thing it's another. First I lose the ability to publish anything for a week and then the next week my laptops charger goes missing, which took me a week to friggen track down. This has been a great start to this story, huh?**

**Also, feel free to point any errors you see. My "editor" (by editor, I mean family) has been unable to read any of my stuff lately, so if you notice it and it bugs you, point it out and I'll correct it (unless I did it on purpose).  
**

The three of them had been brought back to the same interrogation room they had been in before. Dad had settled down immediately, digging into several files, spreading schematics all over the metal table top. Jack was leaning back in his chair, his ankle on his knee, and had whiled away the time chatting idly.

As for Jenny herself, she was shooting dark glares at her father from time to time as she talked with Jack. Dad could be so annoying. It was bad enough that he always thought he knew what was best for everyone, though to his credit, he usually did, but he got so childish about it if he wasn't getting his way. Not only was he always trying to protect her from harm, now he thought she was some kind of infant that had to be watched all the time.

She returned her thoughts to Jack's conversation. "So he really thought you were psychic?"

"Yep. I mean, it helped that I had his name, but it was simple. Alonzo was sweet, kind, but far too easy to read." Jack grinned. "It ended badly, of course. You can only keep a charade like that one for so long before it comes to light. There was all the usual stuff, screaming, yelling, throwing things out of the airlock. He, of course, accused me of lying and not ever caring about him, I said he was being too sensitive and needed to embrace life more."

Jack let his leg down and sat up a bit. "He was wrong, of course. I did care about him. Maybe not as much as I should of, but I did." His eyes looked sad. "When you get to be as old as I am, it gets harder to find that kind of a relationship. I don't mean sex, mind you. Sex is easy. Dime a dozen, as they say. But to be in a real relationship, for however long, that's difficult. I've seen so many people grow old and die, if they're lucky. Just plain die, if they're not. It get's almost intimidating." There was a sad chuckle. "Sometimes, I really do miss the ignorance of youth, where everyone seems immortal, not just you."

"You don't look that old."

Jack flashed her a genuine smile. "Thank you. Of course, that's because I have something I have in common with the Doctor. We're both a lot older than we look."

"So you're a thousand years old too?"

"Oi," Dad protested, looking up. "It's nine-hundred."

"And change," Jenny retorted.

"If not more," Jack said, grinning again. "I think he lost track a while ago."

"Do you both mind?" Dad scowled.

"Sorry," Jack said, holding up his hands. "Have you figured it out yet?"

Dad grumbled.

"Is it really that difficult?"

"Yes," Dad snapped. He sighed. "It's like a puzzle. Except I don't have a picture and they only gave me half the pieces."

"Half the pieces?" Jenny asked.

"Not everything was stolen. Yes, a lot of the big, shiny, special pieces were, but there are several things that you can just easily go down to the shop and buy. Copper wiring, link cables, anything." He held up a sheet of paper. "This here is high energy fuse box, military grade. You'll find them in the _Valiant_. I can think of two-hundred and seventy-eight different uses for it." He glanced at it again. "Two-hundred and seventy-nine." He put the paper down. "Even with all the pieces, there is still fifty-four different possible machines I could build."

"Is there a pattern?" Jack asked.

Dad shook his head. "It could be anything from a computer to an energy transfer to a low level sub-light drive." He shifted some of the papers around. "To figure out what they're building, I would need both what they stole and what they bought. To find out what they bought, I need what they stole and what they are trying to build. Without either of them, I left to flounder."

"So now what?" Jenny asked.

Dad picked up another sheet of paper. "I don't know."

"That's it?"

He nodded.

"You're not giving up, are you?" Jack asked cautiously.

"Give up?" Dad let out a soft snort. "Of course not. When have you ever known me to give up?"

"Good." Jack stood up and stretched, glancing at a clock on the wall. "It's almost ten. I'm guess we'll be up most of the night, so I could use some coffee. You guys want any?"

"What's coffee?" Jenny asked curiously.

"Honestly, what kind of planet did you grow up on," Jack joked. "It's a stimulant, full of caffeine. If you want, I can get you a cup with plenty of sugar and cream. It's kind of an acquired taste, so you probably shouldn't start on it straight."

"Sure."

"Doctor?"

Dad shuffled several more papers. "Tea, if you don't mind."

As soon as Jack left, Dad slowly put the papers he was holding down, looking over at her. Jenny crossed her arms.

"Okay, so, about Jack," he began. "You have to realize, Jack's from a century where things were freer. People would," he paused. "Okay, when a man loves a woman-"

"Are you really trying to give me the sex talk?" she interrupted.

He hesitated. "Yes?"

"Dad, I already know all of that."

His brow furrowed. "How?"

"The machine wasn't completely useless, it wasn't just military stuff. It taught me about reading, writing, maths, sex. The last part was kind of important. There's not much point in popping out full grown adults without it."

"Okay, maybe, but there's a big different between knowing about it academically and actually-"

Jenny let out something between an annoyed snort and a sigh. "Dad, I'm not a child."

"You're not even a year old yet, I think that qualifies."

She leaned across the table to glare at him. "I am an adult. I can make adult decisions. I don't need you to keep trying to baby me."

"Jenny, I'm your dad. It's what we do." He shook his head. "Look, I'll admit to doing some stupid things as a kid, especially in my first century, and I just don't want you to repeat my mistakes."

Her retort was cut off by the door opening.

Pritchard hesitated. "Uh, hi. Doctor, you test is kinda done."

"Kinda done?"

"Well, no, done-done, so like the info has been processed, but, well, it hasn't been tested yet."

"Good." Dad stood up and gathered up all of the schematics. "We'll finish talking later," he murmured just soft enough for her to hear it.

She scowled at him.

The folders tucked under his arm, he followed the young tech back to the lab with their armed escort. He settled down at the computer, clicked through the data and then smiled. "Marvelous."

"What is it?" Pritchard asked.

"A break through, maybe" Dad answered. "Is there some way I can put this on a bigger screen."

"Well, yes," Pritchard nervously fiddled with some controls. The room darkened and suddenly the screen was projected against the only blank space of wall between several machines. "So, I mean, if you don't mind, what's this break through?"

Jenny noticed Sloane enter the room out of the corner of her eye as Dad started. "So these here are the DNA from my third regeneration and our Mystery Doctor." One the wall, there were two windows of repeating letters, GCGCATTAGCCG and so on, row after row. "They're lined up so they match. These here are the phenotypic genes." The windows seem to spin as the letters flash past, coming to a sudden stop. "As you can see, they're different." Jenny decided to take his word on it, since they both looked like groups random letters to her. "That makes sense, of course, since they're supposed to be different regeneration. However, then there's this." Against the letters flew by then stopped suddenly.

Pritchard was squinting. "Wait, so, wait, that, well, that can't be."

"Would you mind explaining this so that the rest of us can understand?" Sloane asked.

Dad glanced back at him but didn't seem all that surprised by his appearance. "I see you've decided to join us again."

"One of the guards radioed about a break through," Sloane rumbled. "My office is just down the hall. Now please answer the question."

Dad highlighted a series of letters on the screen. "The problem is this. This gene here doesn't exist."

"What do you mean, it doesn't exist?"

Another set of letters in both windows were highlight in a different color. "The genes before it match." More letters were highlighted. "The genes after it do too. But suddenly, inside our Mystery Doctor, a Mystery Gene appears, one that doesn't appear anywhere in my own DNA. And it's not the only one." The screen flashed again, pausing to highlight something, and flashed forward again. "All in all, there are seven genes that don't match any of mine. Granted, that's seven out of hundreds and hundreds, but none the less. You're computer didn't know what to do with them, so it just expressed them as an error. A point oh-oh-oh-oh-five percent difference."

"But, well, that could mean a lot of things," Pritchard butted in. "Mutation, for instance."

"You're right," Dad said with a nod. "However, they do match these." A third window opened, flashing passed letter, pausing only to highlight a few.

"Whose are these?" Sloane asked.

"This is Jenny's. All seven Mystery Genes from our Mystery Doctor are in her as well."

Jenny blinked. "What does that mean?"

Dad glanced over at her. "They're false genes."

"Progenation."

"What's progenation?" Sloane interjected.

"Progention is a way of making new people. A sample of my DNA was taken, split apart and recombined to make Jenny. But doing that damages the DNA, so they inserted false genes to fix the problems."

"So this Mystery Doctor is progenated? So why does his DNA match yours so closely?"

"Because he was cloned." Dad leaned back. "A couple of months ago, Jenny and I were on a rather nasty station run by a rather nasty man. He trapped people there and put them in impossible and lethal situations for his own amusement. If you died, he used several re-purposed progenation machines to create a clone of you with all the memories you had up till that point." He paused. "I regenerated on that station. One could argue that in regeneration, there's a moment when I would die. If the system picked up on that and created a clone of me in the middle of it, well, it wouldn't be pretty. Regeneration is a risk process in the first place, but you add it being started suddenly with its energy level already too high, coupled with new genes tacked on, it could very well cause the entire thing to go wr-"

Dad went still for a moment. He slowly straightened in his seat. "So that's how it happened," he murmured.

"That's how what happened?" Jenny asked.

Dad blinked and looked at her with wide eyes for a moment. "Hmm?" He shook his head. "Sorry. Okay, yes, that must have been what happened."

Jenny's eyes narrowed. He was keeping something from her.

He was looking around. "Where's Jack?"

It was the rest of their turns to blink. "What?"

"Jack. What happened to him? He went to get coffee and never came back."

"Maybe he got lost?" Jenny offered.

"No, not Jack." Dad got up suddenly and hurried out of the room, the rest of them trailing behind him.

They ended up in a break room, causing a rather startled soldier to jump to her feet in a solute. "At ease, Corpral," Sloane said. She let her hand fall to her side.

"Have you seen Jack?" Dad demanded.

"Sir?" She looked from him to the General.

"Jack," Dad repeated. "Tall, brown hair, hazel eyes, cleft chin."

"Oh, the pretty one," she said, a soft smile touching her lips for a moment. Then she coughed uncomfortable. "-sir. Yes sir, I saw him. He came in to get some coffee."

"What happened to him?"

She shrugged. "He got a phone call and left."

"That's it? He just left?"

"Yes sir."

"Okay, fine. What was the phone call about?"

"I don't know sir. I didn't want to be rude."

Dad sighed. "Honestly, what's wrong with you lot. Rule number fifty-seven of the universe. Always eavesdrop. It makes my life so much easier."

"I sorry sir." The Corporal hesitated. "I don't think he knew the person, sir. He asked who it was. I didn't hear anything after that."

"Yes, because that's a lot of help."

"Doctor, is this really that important?" Sloane asked.

"Yes."

"Then we can listen to it."

"Excuse me?"

"We monitor all the calls that go in and out of UNIT Head Quarters, even cell phones. We'll have a record of it in the Communication Hub."

Dad shot him a dirty look. "Okay, rule number three. Don't leave the Doctor out of the loop."


	5. Phone Call

At first, Jenny mistook the Communications Hub for a command room. It had several large screens displaying a great deal of information, as well as approximately twenty of so people scattered around at different tables. At a second glance, however, her military side told her the layout was wrong. A good command room had a single point of reference, usually a map or some other piece of important information, with outlaying information sources around the outside edge. Sometime that it would be a circle, with the map in the center. Other times it would be rows in front of a screen.

The Communications Hub was a square. In each corner was a round table with six stations, all of them only partially full. That wasn't surprising when you figured what the local time was. There were four screens, suspended above the actions in the middle of the square, facing out in each of the four directions.

Sloane tapped the shoulder of a tech at one of the stations and spoke into his ear. The tech nodded and began tapping away on his computer.

Jenny glanced at Dad. He was impatient, she could tell. He had this way of fidgeting that made him look like he was pacing even though he was standing still. Their escorts were leaning against the far wall, trying to remain out of the way.

"I'm sorry sir," the tech was saying. "I seem to be having a bit of trouble finding any phone registered to Captain Harkness. I have him on video but I can't seem to find the call information. You'll have to give me a moment."

"Blasted Torchwood," Sloane grumbled. "The Devil take them."

"He probably would," Dad said, glancing at the screens as if trying to distract himself.

"It's a figure of speech, Doctor."

"Yes, but that doesn't change the fact he would." He gave the general a wry smile. "Met him once, the Devil. Nasty guy. On a nasty planet too. Then again, I can't think of many nice planets orbiting black holes. Magnificent view, though. It's not every day you get to see the event horizon of one and live to tell the tale." He paused. "You don't like Torchwood."

Sloane let out an annoyed huff. "No Doctor, I don't. My job is crowded enough. Between the CIA and MI5 overstepping the bounds on a regular basis, and those idiots in the regular UN forces that don't seem to understand that just because we work for the same organization, they're to keep their noses out of extraterrestrial matters, plus freelancers like you and your protégés, like Sarah Jane Smith, we're forever trodding on each others' toes. I can forgive the former because pissing contests are to be expected in any form of law enforcement. I can forgive the latter because of how much you've done for this planet and because I doubt anyone could be dragged along on adventures with you and not be inspired to try and copy them."

He adjusted his collar before continuing. "Groups like Torchwood are a step too far, however. We may all bend the rules to get the job done, but they believe they're above them. To be honest, I was relieved when the last of the Torchwood teams that hung on after that debacle called Canary Warf disbanded. Therefore, I hope you can imagine my dread when I heard the Captain Harkness had reappeared a year ago. The first thing he did was pick up his old colleague, and set about rebuilding. I had been moving to block them off, prevent them from reestablishing their old contacts and hiring new members, but then this entire thing took precedent. Of course, now it's too late. To be honest, it would make my life a great deal easier if they simply disappeared."

"Whatever your personal beliefs in the matter are, Jack is a good man." Dad's voice was barely more than a whisper. "I will not leave him to whatever fate has captured him."

Sloane seemed to hesitate. "I understand my duty perfectly well, Doctor, and I don't need you to remind me of them. Whatever my preference in the matter are, that much is clear." He paused. "You think Harkness was captured."

"I know Jack. Very few things would have caused him to leave the building right now."

"I see."

"Sir," the tech spoke up. "I found it. The quality won't be quite as nice as I would have liked since I had to get it through a back door of sorts, but I cleaned it up a bit, so it should sound fine."

Sloane nodded. "Play it."

An image of the break room flickered onto the closest screen. Jack was busying himself with at what Jenny figured must be the coffee dispenser. He reached into his pocket and put a phone to his ear.

"Hello?"

"Hello Jack."

"Who is this?"

"Jack, I'm hurt. I suppose it makes sense that you don't recognize my voice, though. I have regenerated again." Jenny glanced at Dad. It wasn't his voice. It was lower, and seemed to have a charming purr in it. It was the kind of voice that would make you want to listen to the speaker. Despite that, there was something about it that sent chills down her spine. "It's me, Jack. The Doctor."

On the screen, Jack turned away from the coffee dispenser and faced toward the wall. "No you're not," he said in a quiet voice.

"It really is me, Jack. I promise."

"You're not the Doctor."

"If you make me prove it, it'll hurt my feelings. After all the times we've had together, in World War One, on Station 500, at the end of the universe, and that whole charade with Davros. Not to mention Kyoto." There was a pause. "Look, Jack, I've been back in town for a while. I meant to get in contact, but you know how things can get. I just finished a project, though, and I thought you might like it. I was going to ask you over, but I found out you were at UNIT Headquarters. They're certainly a boring lot, with all the saluting and marching toward their deaths. I'm surprised the UN hasn't just gotten rid of the berets and just given them red uniforms instead. It certainly would make the purpose a lot clearer. But I'm getting off track, you shouldn't let me do that. None the less, since I couldn't reach you, I decided to invite some of your co-workers to come by. Several new faces, I've noticed."

Jenny couldn't see his shoulders tense in the poor quality of the video, but she heard it in his voice. "If you've hurt any of them-"

"Don't be so cliché, Jack. They're absolutely fine. For the moment. Unfortunately, I've made some new friends of late. Not quite the usual group, but useful for certain situations. At least as long as their bill's been paid. However, they can get restless, and to be honest, the less time your friends spend in the company of mine, the better it will be for everyone."

"How do I know you're not lying?"

"Must you?" The voice sounded a little strained. "This isn't some pathetic crime show on the telly. I have no reason to lie to you nor do I particularly want to sit around while you run through every cheap Hollywood plot your lot comes up with."

"Prove it."

There was as exasperated sigh. "If you insist."

"Jack?" a woman's voice asked. "Jack, you can't come here, they-" There was a loud crack and a cry of pain.

"I believe I just said I didn't want a cliché," the Mystery Doctor said in a muffled voice, probably due to holding his phone outstretched instead of to his ear. "Yet you insisted on that. You could have kept her from talking in several different ways. Use one of them next time."

There was a rustling and his voice became clearer. "As I was saying, it really would be best if you got here as soon as possible. They really aren't the brightest blokes, and I really would hate it if anything happened."

"What do you want?" It sounded as if Jack said that from between clenched teeth.

"I told you already. I want to show you my new project. It won't take long. Afterwards, you, Miss Cooper, and the rest of your team are free to leave."

"Just like that?"

"Yes, just like that. Neither I nor any of my friends will try and stop you."

There was silence for a moment. "Okay, fine. You win."

"Jack, this isn't about winning or losing. It's just a nice reunion between friends. One stipulation, though. Don't bring anyone from UNIT. Don't even tell them. They're far too pathetic to even bother with and I most certainly am not inviting them." There was a pause. "I seem to have misplaced the address. It's impossible to remember, all these warehouses look alike. No matter, I'll send it along soon enough. I would suggest, however, you head off now. Time is, after all, of the essence."

On the screen, Jack hung up. He turned around and left the break room, nodding briefly to the corporal sitting at the table. She watched him leave, hiding what was probably a smile behind a cup of coffee.

"That was certainly informative," Sloane muttered as the screen went dark. "Do we have the address?"

"Not yet sir. It looks like it was sent as a text after Captain Harkness left the building." The tech looked from his screen to the general. "I have his number now, however. If you give me a moment, I should be able to track it down."

"Do it."

"I take it this exonerates me," Dad said, still staring at the screen.

"Yes, Doctor. I apologize for this entire situation."

"I have it sir," the tech chimed. The address flashed across the screen.

"Not far," Sloane mused. "Contact with Colonel Magambo and tell her to get all of her units ready. We're going in."

"No, you're not," Dad said.

Sloane, who had been in the middle of turning toward the exit, stopped. "Excuse me?"

"You heard him. There are hostages. If you go in, they'll die."

Sloane was scowling. "Yes, Doctor, my shoulder might ache, but my hearing is fine. Despite what you may believe, UNIT is trained to handle situation like these. We can handle it."

"Not against him, you can't."

"And who is he, Doctor?" Sloan snapped. "You've known since your little display in the lab, that much is clear. If you think my mind is so addled I didn't catch you're little slip there, you are sorely mistaken. I don't like being kept in the dark any more than you. So, please, enlighten us. Who are we facing?"

"Me." Dad shifted slightly. "In a matter of speaking, at least. You're facing a wrong-me. A me who never should have been, yet a me I knew was coming." He locked eyes with the general. "Despite whatever you think about what I think, let's get the facts on the table. I'm good. I am so far beyond what a mere human that very few people on this planet could even begin to match me. And he's just as good as I am. If you go charging in, things are going to end very, very badly. And you know it."

Sloane's temple was bulging again, but he remained quiet.

"It'll mean the deaths of the hostages," Dad continued. "And it'll mean the deaths of your soldiers."

"So what is your suggestion, Doctor?"

"My suggestion, if that's what you want to call it, is to let me go in and take care of it."

"No."

Dad's eyes flashed. "You're forgetting, General, about what I can do if you try and stop me. I won't let military foolishness risk peoples' lives."

"And you're forgetting, Doctor, that this is our investigation. You were brought in as a suspect, and of that you have been cleared. The rest is left to us."

"Do we really have to keep doing this?" Jenny demanded. "Honestly. Look, if this Wrong-Doctor is as good as Dad is, then do you honestly think you could stop him? Especially since he doesn't seems to have the same morals as Dad?"

Sloane ground his teeth. "No."

"That doesn't it make sense to let Dad take care of it. Or at least try too? Think of how many lives it could save."

The general seemed to mule that over. He glanced at a watch. "Fine. It's currently twenty-two forty-five. We'll most likely arrive at the scene at twenty-three thirty. I'll give you till midnight to take care of this, Doctor. If you haven't by then, I'm coming in."

"That'll only give me a half an hour, but fine, if you insist."

Sloane raised an eyebrow. "We'll release the TARDIS to you if you need more time."

Dad shook his head. "He'll sense it if I use it to get close to him, and that's the last thing I'd need."

Sloane nodded slightly. "If I'm going to be reduced to being support for the moment, is there anything else you're going to need?"

"No. I'm going in there alone. Anyone or anything else would just get in the way."

"Like hell you are," Jenny snorted. "I'm going with you."

"Jenny-"

"No, Dad, you don't get to order me away from this one. You heard him. He's got hired guns. What are you going to do, distract them with a wind-up mouse? You're going to need someone who's trained to fight."

"I don't need a soldier here, Jenny."

"Who said anything about being a soldier? I'm not going to bring a gun. I'm just going to knock out anyone carrying one. That sounds more like a warrior to me. Maybe an infiltrator. A spy. A-"

Dad let out a low growl. "Fine."


	6. Warehouse

**Author's Note: DOUBLE FEATURE? WHAT? Actually, this is because I did a terrible job planning out the chapters this time around. 6 and 7 were supposed to be the same chapter, but ended up being as long as two, so I split them up.**

It was the thrumming in his head that woke Jack up. It was the sort of headache that made you want to curl up with an IV of morphine pumping directly into your skull, the needle stuck somewhere between the pounding jackhammers and the scraping drills.

He managed to crack one eye open enough to let light flood in, causing even more pain.

He groaned.

Slowly, he forced his eyes open, trying to ignore the searing pain in his head. A person didn't die as often as he did without picking up a couple of tricks. After a few moments, the pain started to subside enough that it was possible to think again.

"Jack." It was a woman's voice, in a tone suggesting that wasn't the first time she had called his name in the last few minutes.

He tried to look around, still squinting slightly. "Gwen?"

"It's me, Jack." There was a note of relief in her voice. "I'm over here."

She was handcuffed to a railing running against a far wall, half standing, half hanging, her hands above her head. She wasn't alone either. The entirety of his new Torchwood team was there, Billy, Rachel, Nadia, and Zack, each handcuffed in the same way.

"Is everyone alright?" he asked.

Gwen smiled. "We're fine, Jack, all things considered."

Jack glanced around. They were in a large room, almost pointlessly large. It was old and dirty, and shrouded in darkness. There were only two lights, one that descended from the darkness of the high ceiling to hang above Jack and another that dimly illuminated a door. Jack could see several more dark shapes that looked like industrial floodlights perched on nearby walls or sitting atop their own stands, but they were all dark.

As for Jack himself, he had been strapped to a slanted table, without his shirt of course, his wrists, feet, knees, and waist secured tightly. He tested each of the lightly to see if any of the straps were old or frayed enough to be broken. They weren't.

He looked back at Gwen, noticing that it wasn't a railing that she had been chained too, but a sturdy old pipe. "Where are we?"

"I don't know," she admitted.

"What happened? I mean, how did they get you?"

"I don't know that either. I was at home and suddenly I got hit from behind. Woke up here."

"They grabbed you at home? Did they hurt-"

She shook her head. "No, Rhys and the baby were visiting his mother."

Jack smiled slightly. "Good." He glanced around again, looking for some way out. "You know, when I started the team back up, this wasn't what I was expecting."

"Really? I was."

Jack let a little laugh escape. "Then why did you say yes when I asked you to come back?"

"For the same reason I joined up in the first place. Because someone has to keep an eye on all these crazy aliens running around."

"You could have always joined UNIT?"

Gwen snorted. "You just want to see me in one of those red berets."

"You know me."

A moment passed.

"I'll admit," Gwen said, her voice serious again, "I wasn't expecting something like this so soon. We've barely finished getting the Tower back up and running, and training the team. I was hoping to start with an easy first case, maybe a Weevil or something."

"Yeah."

"Jack," Gwen's voice has taken a hushed tone, "he says he's the Doctor."

"I know."

"He looks different."

"He can regenerate instead of dying. It gives him a new look and a new personality."

"So he wasn't always like this?"

Jack hesitated. A quick look around didn't reveal anything. "Gwen, this isn't the Doctor."

"Jack, I'm hurt." The voice echoed from above them. The flood lights flared, blinding Jack for a moment. Footsteps echoed on metal from the farthest wall, then they descended what sounded like a small set of stairs, before crossing the concrete. He stepped just inside the rough circle of light the floods were creating. "I don't know why you're so adamant in your denial. Can't you just accept that everyone changes a bit?"

Jack focused his gaze on this new Doctor. He was tall with brushed back, gleaming red hair. His face had a sort of rough-worn handsomeness to it, as if it had been carved by a talented artist with a dull chisel and he was dressed in a sharp black suit. He looked like a lawyer or a politician, and he wore a well crafted look of hurt on his face. It didn't reach his eyes.

"I think this is a bit more than a bit."

The other Doctor waved his hand in a dismissive manner. "I'm sorry about the hit on the head. Like I said, my new friends can be a bit rough."

"Yeah, well, thugs'll do that."

"Unfortunately. However, I still wish to show you my project."

"Project." Jack looked around. "You know, I'm not really seeing much of a project. I mean, yeah, you have me restrained and laying on a table, but that sounds like a run of the mill Saturday night for me."

The other Doctor let out a chuckle that seemed as empty as his eyes. "That does sound like you." He walked toward them, moving with a sense of purpose and a gate that belied much more muscle than his suit let on.

He stopped, laying one hand on something behind Jack. A cold pit began to form in Jack's stomach. Due to the table's angle, he couldn't see what was directly behind him. But whatever this project was, he was strapped in it.

The other Doctor's face was not far away from his. At this distance, Jack could see the lines of malice around his eyes and brow. It was a face that never smiled, and least not genuinely.

"I won't deny, Jack, I'm rather jealous of your gift."

"What gift would that be? My stunning good looks? My raw sexual prowess."

"The fact you cannot die, Jack."

The pit in his stomach got colder. "Oh, that. It's not as great as it seems."

"Really?" The other Doctor began to fiddle with something behind Jack. "Even a bullet to the head can't kill you. At least, not permanently. What is it like, Jack, to die and come back to life?"

"Painful. You've regenerated enough times to know that."

The other Doctor let out a sigh. "Yes, that." He pulled a bundle of electrodes out and began to attach them. "It's not a terribly great way to cheat death, unfortunately. Every time it happens, I'm forced to change. And I don't have very many left in me. But you, you stay the same. No matter what happens, you stay alive and stay the same." He paused. "I'm running out of lives, Jack."

"So you want mine."

The other Doctor gave him a fake smile. "That's what this entire project is about, yes." He placed a wire crown on Jack's head. "I'm sure you understand."

Jack glared at him. He stared back unconcerned. "You're not the Doctor," he finally growled between clenched teeth.

The other Doctor gave a good imitation of a hurt sigh and reached back to something else on the machine.

"And he will stop you."

The other Doctor froze and locked eyes with Jack. "Excuse me?"

The dimly lit door slammed shut. "He said that I'll stop you."

The other Doctor turned around very slowly. The Doctor stood in the dim light, his hands in his pockets.

"Who are you?" the other Doctor asked.

"I'm the Doctor," the real one answered.

Jack expected a dozen different reactions. Just not the one he got.

The other Doctor laughed. Not the empty chuckle from earlier, but a real one filled with amusement. Oddly, that didn't make Jack feel any better. It sent a chill down his spine.

"Are you now? Well, that certainly explains Jack's refusal to see reason earlier." He let his arm drop and fully turned to face the real Doctor. "What exactly makes them think you could possibly be me?"

The Doctor started toward the circle of light. "Well, the two hearts help. The screwdriver too." He held up the silver tool. "Plus the fact I have some time and relative dimension in space bundled up in a blue box."

"So you're why the TARDIS left. For some reason, I thought she had abandoned me for no reason. Quite annoying, I might add. I took me a while to track down someone to give me a Vortex Manipulator."

"Yeah, I'm sure you didn't murder the Time Agent who had it to get it," Jack said bitterly.

The other Doctor didn't answer him and continued onward. "I'm a little surprised, of course. I never expected to meet someone who was a good enough double to fool my ship."

The Doctor stopped just inside the light. "You really don't understand, do you?"

The other Doctor shifted. "What exactly am I not understanding?"

"I didn't trick the TARDIS. I really am the Doctor. You're not."

The other Doctor face went from amused to annoyed. "Are you now? And why do you think that?"

The Doctor shook his head. "Does this really look like something I would do? Strap my former companion and a very good friend to a machine that, to be quite frank, is going to kill him. To drain him of all of his energy."

The other Doctor shifted again. "You know what this machine is designed to do."

"Once I knew who I was going up against, it was easy. You really expect me to believe you can justify murder?"

"Yes." The other Doctor took a step forward. "I have done much for this galaxy. I've saved it time and time again. And it has killed me, so many times. Once I can no longer die, that won't matter. I'll be free to save countless lives."

"So the end justifies the means?"

"Yes."

The Doctor face was a mask, showing no emotion. His eyes, however, were sad and angry. "The means are all that matters. I won't deny that I've done so many terrible things. They haunt me, the screams of the damned. I cannot and will never hesitate to do what must be done." He seemed overwhelmed for a moment. "But that's when I have no other choice!" he barked, his voice strong again. "The end is nowhere near as important as the means to it. I would never, never do this. It would make me no better than the monsters I've had to stop."

The other Doctor sighed. "I sense there is a very large gap in our philosophical beliefs here. I dread the idea that this might devolve into another Bentham versus Kant debate."

The Doctor grinned suddenly. "What's wrong, waiting for you, what did you call them, friends?"

The "Doctor" looked up sharply.

"Sorry, I don't think they'll be joining us. The few of them that are conscious probably are too embarrassed to show their faces after being beaten up by a 65 kilogram girl."

"Hey!" Jenny seemed to appear out of the darkness like a ghost, not far from her father. "I'm only 55 kilos."

"Jenny," the other Doctor murmured softly.

She looked at him. "So this is the fake guy, huh?"

His neck stiffened. "Not only did you take my ship, but now you've turned her against me as well." In one swift motion, he pulled out a pistol. Jack recognized it as a .45 caliber Glock. "You are beginning to become more than an annoyance."

"Okay, yeah, that'll work," the Doctor said, raising his hands and rolling his eyes at the same time. "Nothing spells out 'Doctor' like a gun, because there's nothing more I love than one of those. Not like this little thing here." He wiggled the sonic screwdriver that was still in his hand.

"Yes, that thing," the other Doctor said with contempt. "I grew sick of using such a passive-aggressive weapon. And make no mistake, as she once pointed out, it is a weapon."

The Doctor shook his head. "You really don't get it. Okay, let me try to explain this again. I'll us smaller words, don't worry. I am the Doctor. You are not. If you want proof, think back to when you regenerate. Wait, sorry, that was a big word. Okay, think back to when you died and then came back to life. Where were you after? Because I'm betting you were alone in a little tiny machine in a big empty room. Am I right?"

The other Doctor didn't answer.

"Do you want to know where I ended up after I regenerated, because I'll tell you. I was right where I started, in front of Jenny, and Marla, and Carlos, and Charles. And a giant killer robot, but that last one is beside the point. Do you get it yet? I'm the Doctor. And you're the Valeyard."

Jack jumped as the other Doctor screamed, "I AM NOT THE VALEYARD!" Quite suddenly, the calm, composed, and charming man was gone, and a mad-man stood in his place.

"But you are," the Doctor shot back. "You're the little coward so obsessed with his own mortality that he tries everything he can to get an extension by any means necessary. You were then and you are now."

"NO!" The Valeyard took a deep breath. "No," he repeated more calmly. "I am the Doctor. I will, however, admit that you seem to be as well. Unfortunately, there really can't be two of us running around, now can there."

Jack never even had a chance to yell out a warning.

The pistol barked.

Whatever Jack lacked in speed, however, Jenny more than made up for. As quickly as the gun kicked, she moved to the Doctor's side, throwing him aside with her shoulder.

And the bullet slammed into her chest.


	7. Departure

**Author's Note: I'm nervous again. But on the plus side, I just added a FAQ to my profile. That might answer a couple of questions.**

"NO!" The Doctor and Jack cried at the same time.

The Doctor struggled up and caught her just as she fell. He clutched her to him, staring down with horror. "You little idiot. Why?"

"Why?" the Valeyard echoed. Jack glanced at him. He was trembling. "Who jumps in front of a bullet twice?"

"Apparently she does," the Doctor said softly.

Jenny coughed weakly. "Bad habit."

"You little idiot," the Doctor repeated. "Do you want to know I never use guns?" he asked suddenly, not looking up. "Like you said, they're a lot more direct. But do you really know why?" He finally lifted his head and glared at the Valeyard. "Because in the end, it's the people you never meant to that get caught in the crossfire."

Jack had seen the Doctor angry before, but he still marveled in how different it felt. When he had traveled with the Doctor, it had been in his ninth incarnation. Despite their time together, Jack had only seen him angry a few times. But when he was, his emotions were on his sleeve, and he was like a wounded animal, unpredictable and dangerous. He had only taken a few trips with the tenth doctor, but had managed to see him lose his temper as well. That Doctor had burned like a supernova when he was angry, filled with immeasurable levels of fury and unbelievable amounts of passion.

The new Doctor's anger was very different. His anger was cold, calculating, and devastating. It was the kind of anger that crushed its target into nothingness, and even though it wasn't aimed at Jack, he could feel his blood turn to ice.

"I didn't know," the Valeyard whispered.

"That doesn't matter."

Jack could hear stomp of boot in the halls outside. The Valeyard heard it too, looking toward the door. He spared a last glance at Jenny and the Doctor, before lifting his wrist, letting the cuff fall back to reveal his Vortex Manipulator. He pressed it and disappeared in a flash of light.

The door swung open, and soldiers in red berets swarmed in. Jack recognized the colonel.

"He's gone," he explained, struggling with his bonds as Magambo looked at the Doctor for an explanation. For his part, the Doctor was speaking quickly and softly to the dying blonde girl in his arms. "Ran as soon as he heard you. Now will you get us out of here?"

A soldier immediately began to undo Jack's straps as another produced a small set of bolt cutters to free the rest of Torchwood. As soon as one hand was free, Jack pulled the wire crown from his head and began to tear at the remaining straps. Once they were off, he stumbled off the table and rushed to the Doctor.

"I really need you to do this for me," he was saying. "I can't go back to being alone, please Jenny, trust me."

Jenny looked like she was having trouble keeping her eyes open. Her breathing was faint and her skin pale. "Does it hurt?" she asked, her voice barely more than a whisper.

"No," the Doctor said with a smile that didn't even begin to hide the pain in his eyes. "Not in the least."

Jenny's eyes closed and her breathing stopped.

"Jenny." The Doctor shook her. "Jenny!"

And then she started to glow.

Jack blinked.

There was no mistaking it, she was regenerating. But it wasn't like what he remembered, standing in the TARDIS as the Doctor almost died, holding Donna and Rose close. He had released a torrent of energy, bursting out of every exposed inch of skin, before managing to shunt it off into his severed hand. But if the Doctor was a surging waterfall, Jenny was a gurgling brook.

The energy gradually grew brighter and brighter till she looked like nothing more than a bright, girl shaped light. A little flash, even brighter, seemed ripple out from her core to tips of her fingers, before suddenly pulling in suddenly. The glow vanished.

And the Doctor was holding a different girl.

"Jenny?" he asked quietly. "Are you alright?"

Her eyes fluttered open. "Owwwwwwwwwwwwwww." She fixed him with an accusatory stare. "You lied to me. That hurt. A lot."

The Doctor's grin was almost foolish. "I couldn't take the chance you wouldn't do it."

"So you lied?" Jenny pushed herself up onto an elbow, swaying slightly.

"Slowly," the Doctor chided. "It'll take a while to get used to your new body."

After a moment, she managed to get herself sitting upright. She ran a hand back through her hair, pulling out the band holding it back into a pony tail. It fell to frame her face. "My hair changed color."

"Yeah, it'll do that."

She grabbed some of it and held it for closer inspections. "But I liked my hair. It was blonde. Now, it's, it's-"

"Brunette," the Doctor said. "A very lovely shade."

"It's brown."

"Well, technically."

"No, not technically. It's brown." Jack had to admit, her face, split between a frown and a pout, was, at the very least, adorable. It was other things too. "I was blonde. Blonde. Guys like blonde girls."

The Doctor opened his mouth, hesitated, and closed it again. Clearing his throat, he stood up, offering a hand to help Jenny up.

Jack turned his attention back to his team. Free from the pipe, they were waiting as the UNIT soldier worked on getting the handcuffs off their wrists. Gwen walked up to him, rubbing her wrists. They were red and ragged, distorted by the hours chained above her head.

"Are you okay?" he asked.

Gwen nodded. Her eyes flickered to Jenny. "Um, is she-"

"Apparently."

"Oh."

"Colonel," the Doctor said, walked up to Magambo, "we'll need a ride back to UNIT Head Quarters."

"Of course, Doctor," she answered stiffly.

"Congratulations on your promotion, by the way. I hope you didn't have to sacrifice too many innocent lives to achieve it."

She didn't grace him with an answer, only a dark glower, before turning and walking away.

"What was that about?" Jack asked.

"I suppose you could say the colonel and I had a bit of a moral dilemma the last time we've met."

"Over what?"

"Sentient trees."

Jack blinked. "Ah," he said, deciding to pretend he knew what the Doctor was talking about.

The Doctor suddenly changed subjects. "How are you feeling, Jenny?"

"It's quiet," she answered, still frowning.

Jack glanced around at the bustling groups of soldiers, each seeming focused in some sort of task. The room was filled with the sounds of rustling movement, barked orders, and stammered reports. "Quiet?"

"Not here," Jenny said, waving dismissively to the crowd. She pointed to her head. "Here."

"How?" the Doctor asked.

"Well, I always had the military side barking orders." She held up a hand. "It was like 'Rawr, do this, do that, carry a gun, fight, fight, rawr, rawr, rawr'." She puppeted the words with her hand. "And then I had the Time Lady side." She held up her other hand. "It was like 'Hey, have fun, go look at that, what's that do, hey, hey, hey'." Her hand acted that out too. "And they never got along. It was always 'Rawr, fight', 'Hey, have fun', 'Rawr, military protocol', 'Hey, climb that tree'." She paused, staring at her hands. "What am I doing?"

"Acting out a show, apparently," the Doctor answered.

"Why?"

"New body, new brain. You tend to pick up some quirks."

"You mean I'm going to be weird? Like you? I don't want to be weird."

"I'm not weird," he protested. "I'm unique. Eccentric."

"That's weird."

The Doctor grumbled.

"Sir," a soldier interrupted. "The car is ready."

Jack looked at Gwen. "Get everyone back to the Tower. We can talk there. I going to make sure UNIT doesn't hold him up too much." He hurried to catch up with the two of them.

"So, the sides aren't fighting anymore?" the Doctor was asking.

"No, it's like they're not even there." Jenny was frowning again. "I don't know how to explain it. It was like before they were some sort of outside knowledge that was always pressing in, but now it's like a part of me. Like they are there, but they aren't. Am I making sense?"

"Enough," the Doctor said with a smile. "Don't worry, you'll probably have more time to think about it."

Their car was actually a truck. The Doctor, Jenny, and Jack all got in the back, and the engine rumbled to life. Magambo didn't spare them a second glance.

Jack watched the Doctor as the truck bounced down the street. "So tell me, who's the Valeyard?"

"A me. A wrong me."

"You've met him before?"

"In a way. Back in my Sixth Incarnation, I was arrested and framed for breaking one of the Time Lords biggest rules. Non-interference."

"You had to be framed for that?"

The Doctor grinned. "I didn't used to break that rule, but I certainly bent it a lot. Enough to be more than a big thorn in the council's side. He also claimed I committed genocide. I hadn't, of course." His eyes flickered. "Not yet, anyway. I found out later that he was essentially a future, evil version of myself, from somewhere around my twelfth regeneration. We've tangled a few times since then, but I've always won. And that's what terrifies him.

"The Valeyard remembers me winning. By admitting who he is would be admitting he's destined to lose. You have to realized, he's me at my worst. I'm a coward, I know I am. I don't want to die, but I could never put someone else's life in front of my own. He takes it to the extreme." He paused. "I'm only guaranteed thirteen regenerations. I've used up eleven of them, and I may have wasted one with that partial regeneration you witnessed. The point is, I'm only guaranteed one more life. So is he. And that thought terrifies him. He'll do whatever he can to preserve his life. Once I realized who he was, and that you were missing, it clicked into place."

"He wanted to become like me? But didn't you say I was wrong, that I was something in time that wasn't supposed to be. Why would he want to be that?"

"Because he doesn't care. The Valeyard only wants to survive, and he'll do whatever it takes to achieve that. And that's why I'm going to track him down. I have too, before he sacrifices even more lives."

Jack glanced at Jenny. She was examining her hair again and shifting continuously in her seat, looking at her entire body. "What about her? He seemed genuinely upset."

The Doctor's eyes darkened. "Ruminants of my feelings. I'll tear him apart if he comes anywhere near my daughter again."

Jack blinked. "Daughter?"

"It's a rather recent development."

"Oh." Jack made a face. "Wow, yeah, sorry, I thought you two had a completely different relationship. It's a little gross now."

"What did you think we were?"

"Well, you know."

The Doctor stared at him. His eyes flickered away for moment and he blinked. "Oh, Jack. No, just no."

"In my defense, you do have a history with blonde girls."

"Stop, please."

The truck turned into the base, its wheels creaking as they ran along the concrete. After it came to a stop, the Doctor offered a hand to his daughter, who was still busily checking out her new body. "Is everything okay?" he asked.

"I think my boobs shrank."

The Doctor's eye twitched. "Okay, I didn't need to know that."

"You asked."

"Still."

"And I think my butt is bigger."

"It's a very nice butt," Jack offered.

"No," the Doctor said, jabbing a finger at him. "Jenny, why don't you go to the TARDIS? New bodies tend to have different tastes in clothes, so why don't you pick something out."

"Anything?"

"Anything."

The moment she was out of sight, the Doctor turned to Jack. "You're a friend, so I want you to understand. If you lay a finger on her, I'll use the castrate setting on the sonic screwdriver."

"The sonic screwdriver has a setting like that?"

"I'm serious Jack."

He held up his hands in surrender. "I promise."

"Good."

"Is it just me, or is she acting younger though?" Jack asked as they walked into the building, a tall poofy hair soldier holding the door for them. "Less mature."

"Probably. Jenny was created through progenation and programmed to be a soldier. She never got a childhood. This may be as close as she can get."

"So I guess you're not the last Time Lord anymore."

"Well, technically she's a 'Time Lady', but I suppose you're right."

They paused in front of the TARDIS. Jack smiled. "Sloane will probably try and find you, but I can explain it if you'd like."

The Doctor smiled. "Thanks."

The door of the TARDIS opened and Jenny posed. "What do you think?"

Jack's eyebrows went up appreciatively.

The Doctor brow furled.

"Nice."

"NO!"


	8. Epilogue

**Author's Note: Okay, so, anyone else think the last episode had a high HSQ (Holy-S***-Quotient)? I may end up going AU faster than I thought XP Not that I mind, it's had to beat awesome episodes like that... Although, they messed up the glitch in Armstrong's speech.  
**

They had argued for a long time. It was the first real fight they had, reduced to screaming at each other across the TARDIS's control column. It was the first time in a long time that he could remember screaming like that. He wasn't angry, of course. For him, anger was something far worse, and he doubted he could ever bring himself to be angry with her. But he was aggravated. He could feel it in his shoulders and neck, the kind of shaking tension of high emotion. Even now, afterwards, as he was preparing something to eat, he could feel it.

What annoyed him most is that she had a point. He had said she could pick out anything. But he had hoped she would have a bit more sense. People had often accused him of picking out odd outfits, but they had fit his personality, mostly. He had always claimed they were a reflection of himself. And he earnestly hoped that she didn't feel the same about what she had picked.

He could feel her own smoldering temper as she entered. She walked in purposefully, taking a seat at the small table in the kitchenette. The TARDIS had several of them, scattered around, even a large one connected to an enormous ballroom. Her face was set, a determined look of defiance in her eyes.

The Doctor sighed. He had finally laid down an ultimatum, and she had followed it. But only to the letter. However, seeing as they had just had a fight, and he was supposed to be the older and more mature of the two, he let it pass.

The rule had been she needed something to cover her shoulders. When she had first appeared, wearing nothing more than a wide, white band of cloth that went from her armpits to her waist, she called it a tube-top, and dark pants that were far too tight, he had been livid. It was the sort of outfit that left absolutely nothing to the imagination, well, almost nothing, and figuring how young she was, she had no reason to be wearing it.

Most of the argument had descended into him screaming that in no way was she going to be traipsing about looking like a harlot and her screeching that she was wearing more than enough and that he had said she could.

Finally, through gritted teeth, he had ordered her to put something on that covered her shoulders. And she had. Apparently, she had dug out an old suit vest, probably from his third or eighth incarnations, and put that on. It wasn't buttoned up and hid nothing, but it covered her shoulders, so the Doctor had to begrudgingly admit it followed the rule.

Jenny had definitely gotten his stubborn streak, that much was for certain.

The Doctor dished out supper from the skillet, putting half on one plate and half on another. He handed her one of the plate as a peace offering.

She wrinkled her nose. "Eggs and hash? Why do we always have breakfast food for supper?"

He put both plates down, fetched a cup from a cubbard, and started the kettle. "Because I'm cooking. You know, I trained in France once, under some of the best chiefs in Paris. Wonderful food. Except I've forgotten most of it now. End up burning it. But breakfast, breakfast I remember. Besides, I like hash." He settled across the table from her, picked up a fork and gave her a pointed look. "If you'd like something different, then you can cook."

She glowered for a moment before picking up her own fork.

"It could be worse. I could introduce you to fish-fingers and custard."

They ate in uncomfortable silence for several minutes.

"You said you've done terrible things," Jenny said finally, her voice soft. "What were they?"

The Doctor paused and put the fork down. The kettle started whistling, so he busied himself with finishing the tea. "Why do you want to know?"

"Because you said they haunt you. I can tell, you know. When you don't think anyone is looking, I can see it on your face, in your eyes, behind your words. And because I think I deserve to know."

"And why's that?"

"Because we're the last ones, right? The last of the Time Lords. Whatever happened, it was big."

The Doctor stirred his tea, the rhythmic clinking of the spoon against the side of the cup soothing. To be perfectly honest, tea was probably his favorite thing about Earth. There were so many different kinds in the universe, but only here was it so soothing, yet so good at waking up the dull parts of your mind.

"I have seen a lot of terrible things, Jenny. And I've done a lot of terrible things. It a curse of living too long, I think. The universe is magnificent, but it's also so dirty. Just like me."

She didn't say anything. She didn't have too. Her eyes spoke volumes.

He sat down, pushing the plate aside, no longer hungry. The tension from earlier was gone from his shoulders, replaced with the terrible weight of his life. "Do you remember what I told General Cobb on Messaline? About genocide?"

She nodded. "That we'd find a picture of you next to it in the dictionary with saying 'Over my dead body'."

He grinned slightly at the memory before letting it slide off his face. "That was one of the most hypocritical things I've said in my life."

She blinked.

"There was a species called the Racnoss. They were a terrible race that consumed everything in the galaxy. Very early on in our history, the Time Lords hunted them to extinction in a war. But they managed to escape and hide a nursery ship, tucked away in a forming planet. That planet was Earth. And as so much changed for that little world, yet in its very core, thousands of little Racnoss children waited to be born. The Empress of the Racnoss finally returned, not too long ago, and woke them. And up they came, from the center of the Earth, ready to consume the planet and move onto the galaxy. So I killed them." His voice had gotten thick. "All those little children who had never seen the light of day, to save the universe, I killed them. And I watched, oh did I watch, as their mother screamed and cried, and no matter how hard I tried, right then, right there, I couldn't bring myself to care."

He took a sip of tea. "And they weren't alone. I've brought death to so many others, people who didn't deserve it. And then there was the war, the Last Great Time War." His hands were shaking. "The war was hell. It didn't start that way, of course, but it eventually it became the closest thing to hell I think I've ever seen."

Silence settled like an uncomfortable weight. "What happened?" Jenny finally asked.

The Doctor took another sip of his tea. "I've never told anyone about it before. But you're right, it's your history, you deserve to know. It was simple, the plan. We removed the war from time, at least, time relative to the universe. It could rage for millennia, but it would seem like only a mere second to the rest of the universe. Think of it like a giant sphere of time. In the very heart were the Daleks, and outside that were rings of defenses, where the Time Lords and our allies stood. Finally, the outreaches all pulled into one place, one point, that served as out link, our bridge, to the real universe. That was Gallifrey, the home of the Time Lords. Even with our allies help, we were by far the most powerful force on the field, so it made sense." Another sip of tea. "Our allies charged into the heart of the war, a place where time didn't exist in any sense you can understand. Armies would die and come back to life, only to die again. And while that was going on, those rings of defenses would begin to push inward, pressing at the heart until it was gone, and all the Daleks with it. It was the perfect plan, because it wouldn't involve any death. Our allies who died in the heart could be brought back to life, just like that. It really was perfect. Too bad it didn't work.

"Instead of shrinking, the heart started to expand, pressing farther and farther out. By the time they reached where I was, at Arcadia, the war had gotten desperate. So many things were called into existence, poorly thought out and out of control. I tried everything, absolutely everything, but Arcadia fell. I only managed to get a small fraction of our forces out alive. The rest was absorbed into the heart. And when I got back to Gallifrey, I found it had changed. Going in, the Lady President was a good friend, and trusted ally, Romana. But she had been replaced by Rassilon. The new Lord President and I had met before, and despite the fact he was considered by many to be the greatest Time Lord who ever lived, even by our official histories, he was anything but. He was a cruel, corrupt dictator masquerading as a hero. And it was then I discovered in my time away that they Time Lords had become what they fought."

He raised his cup again for a sip, but found his hand was shaking too much. His voice dropped to a very serious tone. "The Daleks are evil. There's no other way to look at it. They feel nothing but hatred for everything that's not Dalek, and will spend every moment of their lives trying to destroy it. They would reduce the entire universe into nothing for their own goals. Rassilon and the Time Lords planned the same. They planned to end the war by destroying time, all time, to reduce the universe to nothingness, so that they could ascend to a higher level of consciousness, above time itself. I wouldn't, I couldn't, let them do that. The universe was far too important. So I stopped them.

"I won't tell you how the Moment works, but I'll tell you what it did. It burned Gallifrey, the entire planet and everyone on it, it burned them from time and space. It severed the link between the war and the real universe, placing it in a Time Lock, forever frozen. I expected to be killed, destroyed by the Moment like everything else. Or, at the very least, to be trapped forever. But it didn't, it banished me back to reality, to spend the eons I had left, alone." Tears actually built in his eyes and he pressed his chin into his palm. "I remembered them. I could hear them, all crying, all those innocent people who were caught with the Time Lords. My allies, my friends, my family. My sons and daughters, my grandchildren, my great-grandchildren. I could hear them screaming." He voiced choked. "It killed me. Both of my hearts stopped, broken little shards.

"But I am such a coward." His voice was filled with scorn now. "Such a pathetic little coward, that when even faced with an eternity alone, I was still so afraid of dying. Still afraid what lay beyond. And so I regenerated. And found myself wandering blindly, trying so hard to forget and so hard to die, yet to scared to commit it myself. But humans, oh humans, they have this way of worming their way into your soul, and suddenly, I had a reason to live. At least, a reason to stop activity trying to die." He gave her a small grin. "And now I've got you."

Jenny was sitting still, her food also forgotten. She had her chin on her fingers and her eyes were wide and disillusioned.

"I'm not perfect," the Doctor continued. "I'm anything but. I will, however, do everything I can to stop anyone from making the same mistakes I did."

She shifted her gaze to the table, staring down blankly. In the long silence that followed, he finished his cup of tea and promptly made another. As he was stirring the cup, she finally spoke. "So now what?"

"Now? Now we keep running. We move forward, and we don't look back. We find Valeyard, we take care of him, and all the while, you'll going to learn."

"Learn? Learn what?"

"Everything. Jenny, I've traveled with lots of people in my life, but they were companions. They weren't ever going to be tied to me forever, they weren't family. Okay, once at the beginning. The point is, you're my daughter and you're stuck with me, and one day, probably so far in the future that you will have long since gotten sick of me, I am going to die. And when I do, you'll inherit it. The TARDIS, the screwdriver, the psychic paper, and everything else. It will be yours to do with as you want. But till then, you need to learn."

Jenny looked thoroughly unimpressed. "Is there going to be homework?"

"Yes."

"Great."


End file.
